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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatatatgttatgatattacttgagatactaaaaccttattcttatgtttgtgatggatcacggtatttgattgctaaatttcacatctcatttttgcagGGGGATCCATTGAAGGTGAAGGTGAACAAACTAACCTCTACAAAGACACAACTTCCTTACTCCTACTATTCTCTTCCTTATTGCCGTCCAGAAACCATAG

Basic information

species Vitis vinifera
transcript Vv11s0037g00210.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0037g00210.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G458845_T01 (Zea mays), 3'ss of exon 1
tatatatgttatgatatt--acttgagatactaaaaccttattcttatgtttgtgatggatcacggtatttgattgctaaat--ttcacatctcatttt-tgcagGGGGATCCATTGAAGGTGAAGGTGAACAAACTAACCTCTACAAAGACACAACTTCCTTACTCCTACTATTCTCTTCCTTATTGCCGTCCAGAAACCATAG
      | ||||||| ||   | |    | || ||    ||  ||| | |||              |   || |  |||| |  |||| |  | ||||| |||||   |||||| |   |||||||||||| || || || || ||||||||||||||||| ||||| || || |||||||||| ||||   ||| | |  ||||
-----ttcttatgatgttttgcatttccttcttaacttgtagccttttatttactgaaatatgttttgcatgttctctaactggttcatagataattttctgcagAAAGATCCACTTTTGGTGAAGGTGAATAAGCTGACATCAACAAAGACACAACTTCCCTACTCGTATTACTCTCTTCCTTTTTGCAAGCCAAACATGATAG

upper sequence: Vv11s0037g00210.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G146951_T01 (Zea mays), 3'ss of exon 1
-tatatatgttatgatattacttgagatactaaaaccttattcttatgtttg-tgatggatcacggtatttgattgctaaatttcacatct--catttttgcagGGGGATCCATTGAAGGTGAAGGTGAACAAACTAACCTCTACAAAGACACAACTTCCTTACTCCTACTATTCTCTTCCTTATTGCCGTCCAGAAACCATAG
      | |||||||   ||   || || ||||| || | || | || |    ||  ||     | | |||    |  | |||| | ||     ||  || |||   |||||| |    ||||| || ||||| || ||||| |  |||||||||||||| ||||||||||||||||| || |  |||   || || |||||||
cagcgaaagttatgaatcta---gaaatgctaaa-ccgtcttataatttagaatggagggcttagatgtttatgagaaatattttatattaaatatcattacagAAAGATCCACTTCCTGTGAAAGTCAACAAGCTGACCTCAATCAAGACACAACTTCCCTACTCCTACTATTCTCTCCCATTCTGCAAGCCGGATACCATAG

upper sequence: Vv11s0037g00210.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA02G36550.1 (Glycine max), 3'ss of exon 1
-tatatatgttatgatattacttgagat--actaaaaccttattcttatgtttgtgatggatcacggtatttgattgctaaatttcacatctcatttttgcagGGGGATCCATTGAAGGTGAAGGTGAACAAACTAACCTCTACAAAGACACAACTTCCTTACTCCTACTATTCTCTTCCTTATTGCCGTCCAGAAACCATAG
 |    ||   || |    | | | |||  || | |     |  |      || |  |   ||     ||||| ||  || |||       |||||  ||||||| ||||| ||||||||||| ||||||||||| || || ||||| ||||| || |||||||| |||||||| || ||||||||||| ||| ||  |||  
ctcctaattcaatcaatgcattggtgatcaaccagagaaacaggccgtgacttttcctaattcgtaacatttgtttattatattgtgt---tcattggtgcagGGAGATCCGTTGAAGGTGAAAGTGAACAAACTGACTTCCACAAAAACACAGCTGCCTTACTCATACTATTCACTGCCTTATTGCCGGCCAAAACACATTT

upper sequence: Vv11s0037g00210.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA06G28090.1 (Glycine max), 3'ss of exon 1
------------tatatatgttatgatattacttgagatactaaaaccttattcttatgtttgtgatggatcacggtatttgattgctaaatttcacatctcatttttgcagGGGGATCCATTGAAGGTGAAGGTGAACAAACTAACCTCTACAAAGACACAACTTCCTTACTCCTACTATTCTCTTCCTTATTGCCGTCCAGAAACCATAG
            | |||   ||||  | ||  ||||  ||  | | | || ||||||  |||   ||  |      ||| | ||       ||   |||    |  |  ||||||||||  |||| |||||| |||||||||||| | || ||||| ||||| |||||||||||||||||||| || ||||| || | |||||    ||| |
acacttccacaatttattaattattgt-ttgattgatctagaatagcttttttcttaaatttac-attaactgtcttatcttat------gttgttcat----tggtgacagGGGGATCTGTTGAGGGTGAAAGTGAACAAACTATCTTCCACAAAAACACAGCTTCCTTACTCCTACTATTCACTGCCTTACTGTCATCCAGGTCACATTG

upper sequence: Vv11s0037g00210.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA17G08130.1 (Glycine max), 3'ss of exon 1
tatatatgttatgatattacttgagat--actaaaaccttattcttatgtttgtgatggatcacggtatttgattgctaaatttcacatctcatttttgcagGGGGATCCATTGAAGGTGAAGGTGAACAAACTAACCTCTACAAAGACACAACTTCCTTACTCCTACTATTCTCTTCCTTATTGCCGTCCAGAAACCATAG
|    ||   || |    | | | |||  || | |     |  |      || |  |   |      ||||| ||  ||  |||    |    |  |  ||||| ||||| |||| |||||| ||||||||||| || || || || ||||| ||||||||||| |||||||| || |||||||| || ||  ||  |||  
tcctaattcaatcaatgcattggtgatcaaccatagaaacaggccatgacttttcctaatttgtaacatttgtttatta--ttttgtgttcattggtgacagGGAGATCCGTTGAGGGTGAAAGTGAACAAACTGACTTCCACGAAAACACAGCTTCCTTACTCATACTATTCACTGCCTTATTGTCGGCCTAAACACATTT

upper sequence: Vv11s0037g00210.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S24_182V6.1 (Physcomitrella patens), 3'ss of exon 1
tatatatgttatgatattacttgagatactaaaaccttattcttatgtttgtgatggatcacggtatt--tgattgcta-aatttcacatctcatttttgcagGGGGATCCATTGAAGGTGAAGGTGAACAAACTAACCTCTACAAAGACACAACTTCCTTACTCCTACTATTCTCTTCCTTATTGCCGTCCAGAAACCATAG
| | | ||       |  | |   |    | |||    | |  |         |    |  || || |  | |  |  |  |||||   |  | ||    ||||| |||    |  | ||||||||||||||| |||| || || |||||||||||||| ||    ||||| ||||||   || |||   ||  | |  || |
tgtttgtggcggacaaacattactgtgcttgaaaaggaagtactgc---caaaacatgttgcgatagtgataacagtaatgatttcgagtggctttgaaacagGGTGATGATGTTCAAGTGAAGGTGAACAAATTAACATCCACGAAGACACAACTTCCATATGAATACTACTCTCTTGACTACTGCACGCCGAAGAAAATTG

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|110713316|gb|EE089129.1|EE089129
EST:     ACGTTCGTTCCTTCTATCTCCCTGGTGTCGCTCCTCAAGATTTCAATAAG                         GGGGATCCATTGAAGGTGAAGGTGAACAAACTAACCTCTACAAAGACACAA
genomic: ACGTTCGTTCCTTCTATCTCCCTGGTGTCGCTCCTCAAGATTTCAATAAGgtatgtctct ... atttttgcagGGGGATCCATTGAAGGTGAAGGTGAACAAACTAACCTCTACAAAGACACAA
EST: gi|161716766|gb|FC067205.1|FC067205
EST:     ACGTTCGTTCCTTCTATCTCCCTGGTGTCGCTCCTCAAGATTTCAATAAG                         GGGGATCCATTGAAGGTGAAGGTGAACAAACTAACCTCTACAAAGACACAA
genomic: ACGTTCGTTCCTTCTATCTCCCTGGTGTCGCTCCTCAAGATTTCAATAAGgtatgtctct ... atttttgcagGGGGATCCATTGAAGGTGAAGGTGAACAAACTAACCTCTACAAAGACACAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttgtgatggatcacggtatttgattgctaaatttcacatctcatttttgcagGGGGATCCATTGAAGGTGAAGGTGAACAAACTAACCTCTACAAAGACACAACTTCCTTACTCCTACTATTCTCTTCCTTATTGCCGTCCAGAAACCATAG
                           tgctaaa  putative branch site (score: 2)
                                         tctcattttt  putative PPT
                   tatttgatt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatatatgttatgatattacttgagatactaaaaccttattcttatgtttgtgatggatcacggtatttgattgctaaatttcacatctcatttttgcagGGGGATCCATTGAAGGTGAAGGTGAACAAACTAACCTCTACAAAGACACAACTTCCTTACTCCTACTATTCTCTTCCTTATTGCCGTCCAGAAACCATAG

- - - - - - - - - - - - - - -taaaacc
- - - - - - - - - - - - - - - - - - - - - - - - - gtgatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgattgc